Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Spi1

Cell type

Cell type Class
Neural
Cell type
Microglia
MeSH Description
The third type of glial cell, along with astrocytes and oligodendrocytes (which together form the macroglia). Microglia vary in appearance depending on developmental stage, functional state, and anatomical location; subtype terms include ramified, perivascular, ameboid, resting, and activated. Microglia clearly are capable of phagocytosis and play an important role in a wide spectrum of neuropathologies. They have also been suggested to act in several other roles including in secretion (e.g., of cytokines and neural growth factors), in immunological processing (e.g., antigen presentation), and in central nervous system development and remodeling.

Attributes by original data submitter

Sample

source_name
FACS-sorted microglia
gender
female
strain
WT
chip antibody
PU.1 (Abcam, EPR22624)
geo_loc_name
missing
collection_date
missing

Sequenced DNA Library

library_name
GSM7273512
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The cells/nuclei were immobilized with Con-A beads and incubated with an antibody overnight. The immunocomplexes were further incubated with protein A-fused micrococcal nuclease (pA-MNase), then digested for 30 min in the presence of 3mM Ca2++ (Ref: PMID: 28079019). If needed, the ChIPped DNA was de-crosslinked and purified by phase extraction. The DNA was filtered with 0.5x AMPure beads to remove unwanted large fragments. Purified ChIPed DNA was then processed to construct a library using SMARTer® ThruPLEX DNA-Seq Kit (TAKARA Bio USA, CA) as the manufacturer's protocol except PCR cycles to avoid amplifying long fragments (13 cycles, 10s for extension).

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
32899349
Reads aligned (%)
29.3
Duplicates removed (%)
31.9
Number of peaks
626 (qval < 1E-05)

mm9

Number of total reads
32899349
Reads aligned (%)
29.3
Duplicates removed (%)
32.3
Number of peaks
616 (qval < 1E-05)

Base call quality data from DBCLS SRA